Rates of Chlamydia trachomatis sexually transmitted infection are stable or increasing and consequences of these infections incur billions in medical costs annually. Vaccines for these pathogens are needed but our limited understanding of how chlamydiae evade the immune system has inhibited progress towards this goal. Chlamydial genomes are small and highly conserved. How these pathogens circumvent immunity, target their preferred tissues and cause disease is unknown. A major reason for gaps in our knowledge was that these pathogens could not be genetically manipulated. Many genes that determine the types of tissues and hosts that different Chlamydia spp. infect may reside in a variable genomic region called the plasticity zone (PZ). It is suspected these PZ genes counteract host cell defenses controlled by the cytokine IFN-. Other results indicate polymorphisms in core genes of C. trachomatis clinical isolates also contribute to immune evasion and disease severity. We recently developed genetic tools that now make it possible to test these hypotheses. In our first aim, we will use a reverse genetic approach to inactivate PZ genes and test if the mutants are sensitive to IFN-, or have other alterations in pathogenicity in vitro and in vivo using a tractable mouse model. In aim two we will use unbiased mutagenesis and forward genetic screens to identify chlamydial genes that contribute to evasion of IFN-. Finally, lateral gene transfer, phenotypic screens and genome sequencing will be used to identify genomic polymorphisms that determine chlamydial IFN- sensitivity in animals and humans.